PDB-9he8: The molecular structure of a beta-1,4-D-xylosidase from the probi...

ID or keywords:

Entry

Database: PDB / ID: 9he8

Title

The molecular structure of a beta-1,4-D-xylosidase from the probiotic bacterium Levilactobacillus brevis

Components

Beta-xylosidase

Keywords

CARBOHYDRATE / beta-1 / 4-D-xylosidase / glycosyl hydrolase family 43 / lactic acid bacterium enzymes

Function / homology

Function and homology information

xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Levilactobacillus brevis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.898 Å

Authors

Linares-Pasten, J. / Logan, D.T. / Nordberg Karlsson, E.

Funding support

Sweden, 1items

Citation

Journal: To Be Published
Title: The molecular strcuture of a beta-1,4-D-xylosidase from the probiotic bacterium Levilactobacillus brevis
Authors: Linares-Pasten, J. / Logan, D.T. / Nordberg Karlsson, E.

History

Deposition	Nov 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9he8.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9he8.ent.gz	692.4 KB	Display	PDB format
PDBx/mmJSON format	9he8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9he8_validation.pdf.gz	457.3 KB	Display	wwPDB validaton report
Full document	9he8_full_validation.pdf.gz	466.6 KB	Display
Data in XML	9he8_validation.xml.gz	85 KB	Display
Data in CIF	9he8_validation.cif.gz	116.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/9he8 ftp://data.pdbj.org/pub/pdb/validation_reports/he/9he8	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-xylosidase

B: Beta-xylosidase

C: Beta-xylosidase

D: Beta-xylosidase

255 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	78.429, 177.180, 78.753
Angle α, β, γ (deg.)	90.000, 98.844, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	1 - 539	21 - 559
2	1	1	PRO	PRO	1 - 539	21 - 559
3	2	2	ASP	ASP	1 - 540	21 - 560
4	2	2	ASP	ASP	1 - 540	21 - 560
5	3	3	ASP	ASP	1 - 540	21 - 560
6	3	3	ASP	ASP	1 - 540	21 - 560
7	4	4	PRO	PRO	1 - 539	21 - 559
8	4	4	PRO	PRO	1 - 539	21 - 559
9	5	5	PRO	PRO	1 - 539	21 - 559
10	5	5	PRO	PRO	1 - 539	21 - 559
11	6	6	ASP	ASP	1 - 540	21 - 560
12	6	6	ASP	ASP	1 - 540	21 - 560

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Beta-xylosidase Mass: 63645.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Levilactobacillus brevis (bacteria) / Strain: DSM1269 / Gene: xynB46, UCCLBBS449_2475 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1L7HA01, xylan 1,4-beta-xylosidase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.08 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: The best crystallisation conditions for the native protein were 27-29 % PEG 1500, 60 to 140 mM Malonate Imidazole Borate buffer, pH 4.0 to 4.5 PH range: 4.0 - 4.5 / Temp details: temperature control

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MAR CCD 300 mm / Detector: CCD / Date: Oct 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.898→47.045 Å / Num. obs: 163853 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC_1/2: 0.989 / R_merge(I) obs: 0.153 / R_pim(I) all: 0.098 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.9→1.93 Å / R_merge(I) obs: 0.898 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 16853 / CC_1/2: 0.578 / R_pim(I) all: 0.717 / % possible all: 87.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.898→47.045 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.903 / SU B: 10.173 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2413	8167	5.001 %
R_work	0.2137	155156	-
all	0.215	-	-
obs	-	163323	97.834 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.425 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.338 Å²	-0 Å²	0.107 Å²
2-	-	-0.536 Å²	-0 Å²
3-	-	-	0.802 Å²

Refinement step

Cycle: LAST / Resolution: 1.898→47.045 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17460	0	0	827	18287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	18045
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15827
X-RAY DIFFRACTION	r_angle_refined_deg	1.503	1.803	24636
X-RAY DIFFRACTION	r_angle_other_deg	0.54	1.76	36505
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.414	5	2176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.418	5	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.307	10	2710
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.646	10	938
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2550
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	21751
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4413
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	2917
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	15231
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	8639
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	9006
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	934
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.205	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.22	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.114	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.678	0.362	8683
X-RAY DIFFRACTION	r_mcbond_other	0.677	0.362	8683
X-RAY DIFFRACTION	r_mcangle_it	1.156	0.647	10851
X-RAY DIFFRACTION	r_mcangle_other	1.156	0.647	10852
X-RAY DIFFRACTION	r_scbond_it	0.991	0.427	9362
X-RAY DIFFRACTION	r_scbond_other	0.989	0.426	9361
X-RAY DIFFRACTION	r_scangle_it	1.643	0.748	13780
X-RAY DIFFRACTION	r_scangle_other	1.643	0.748	13781
X-RAY DIFFRACTION	r_lrange_it	3.995	3.98	19635
X-RAY DIFFRACTION	r_lrange_other	3.974	3.825	19525
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.064	0.05	18919
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.058	0.05	18955
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.068	0.05	18901
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.062	0.05	18929
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.065	0.05	18867
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	18941

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06384	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06384	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05823	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05823	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.0681	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.0681	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06161	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06161	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06492	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06492	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0639	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0639	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.898-1.947	0.384	571	0.355	10447	0.356	12269	0.902	0.917	89.8036	0.34
1.947-2.001	0.324	561	0.314	11083	0.314	12019	0.935	0.939	96.8799	0.291
2.001-2.059	0.313	624	0.287	10862	0.288	11693	0.934	0.949	98.2297	0.261
2.059-2.122	0.295	535	0.275	10596	0.276	11321	0.946	0.954	98.3217	0.246
2.122-2.191	0.307	497	0.255	10326	0.257	10973	0.94	0.961	98.633	0.223
2.191-2.268	0.265	530	0.244	9911	0.246	10601	0.955	0.964	98.4907	0.211
2.268-2.353	0.288	519	0.237	9626	0.24	10261	0.951	0.967	98.8695	0.202
2.353-2.449	0.26	512	0.227	9289	0.229	9916	0.959	0.969	98.8403	0.192
2.449-2.558	0.239	463	0.214	8853	0.215	9424	0.963	0.973	98.854	0.181
2.558-2.682	0.261	465	0.209	8511	0.212	9087	0.959	0.974	98.7785	0.177
2.682-2.827	0.254	500	0.204	8007	0.207	8601	0.961	0.975	98.9071	0.175
2.827-2.998	0.233	371	0.202	7708	0.203	8172	0.965	0.975	98.862	0.175
2.998-3.204	0.21	336	0.191	7226	0.192	7654	0.97	0.978	98.798	0.17
3.204-3.459	0.203	296	0.184	6764	0.185	7146	0.974	0.981	98.7965	0.169
3.459-3.787	0.191	327	0.173	6170	0.174	6584	0.978	0.983	98.6786	0.16
3.787-4.231	0.183	292	0.155	5590	0.156	5955	0.981	0.986	98.7741	0.146
4.231-4.879	0.172	289	0.152	4905	0.153	5271	0.984	0.987	98.5392	0.148
4.879-5.959	0.168	218	0.161	4186	0.161	4466	0.987	0.987	98.6117	0.155
5.959-8.361	0.192	148	0.169	3273	0.17	3470	0.98	0.983	98.5879	0.162
8.361-47.045	0.176	113	0.192	1823	0.192	2007	0.983	0.981	96.4624	0.198

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0873	0.1161	-0.0667	0.2474	-0.0496	0.4054	-0.0181	-0.0294	-0.0159	-0.0106	0.0178	-0.0577	0.0316	0.0453	0.0003	0.2006	0.0425	-0.0016	0.262	0.0151	0.0221	35.709	46.502	18.789
2	0.4534	0.1457	-0.018	0.0797	0.04	0.2345	0.0186	0.0017	-0.0037	-0.0284	-0.0048	0.015	-0.0484	0.0018	-0.0138	0.2116	0.0063	-0.0021	0.2409	-0.0029	0.017	0.329	87.682	-1.06
3	0.3348	0.1616	0.0428	0.087	-0.0184	0.2557	0.0089	-0.0342	-0.012	0.0134	0.0068	-0.0048	-0.0193	0.0187	-0.0157	0.1991	-0.0095	0.0024	0.2767	-0.0138	0.002	11.787	83.012	36.465
4	0.2294	-0.034	-0.1279	0.2199	-0.0526	0.3484	-0.0345	-0.0176	-0.0248	-0.0636	0.0053	0.0291	0.0235	-0.0094	0.0292	0.2417	-0.0003	-0.0073	0.2299	-0.0021	0.0079	2.82	40.662	-1.5

Refinement TLS group

Selection: ALL

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